Interpretive Summary: The bacterium Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) causes Johne's Disease, an economically important intestinal infection of ruminants such as cattle and sheep. M. paratuberculosis is genetically similar to several other types of mycobacteria, many of which are not pathogenic or do not normally infect ruminants. In order to understand what distinguishes M. paratuberculosis from other mycobacteria, we compared genomic DNA from several M. paratuberculosis isolates as well as the closely related mycobacteria Mycobacterium avium subsp. avium, Mycobacterium avium subsp. silvaticum, and Mycobacterium intracellularae. Our results indicate that bovine isolates of M. paratuberculosis are genetically very similar to each other. However, other mycobacteria have several regions in their genome sequence that are different from M. paratuberculosis DNA, indicating that they may lack some genes found in M. paratuberculosis. Other scientists should benefit from the results of this work. They will be able to study the genomic sequences that distinguish M. paratuberculosis from other mycobacteria in order to understand what allows M. paratuberculosis to successfully infect ruminants and cause disease.

Technical Abstract:
Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) is genetically similar to other members of the Mycobacterium avium complex (MAC), some of which are non-pathogenic and widespread in the environment. Despite their genetic relatedness, MAC bacteria are capable of infecting a wide range of host animals with varying pathogenicity. We have utilized a M. paratuberculosis whole-genome microarray representing over 95% of the predicted coding sequences to examine the genetic conservation between 10 M. paratuberculosis isolates, 2 isolates of Mycobacterium avium subsp. silvaticum (M. silvaticum) and Mycobacterium avium subsp. avium (M. avium), and a single isolate of Mycobacterium intracellularae. Genomic DNA from each isolate was competitively hybridized with DNA from M. paratuberculosis k10, and open reading frames (ORFs) were classified as present, divergent, or intermediate. Nine of the M. paratuberculosis isolates had no divergent ORFs, while the remaining isolate had 4 ORFs classified as divergent. 137 and 70 divergent ORFs were identified in the two M. avium isolates, while the two M. silvaticum isolates examined had 77 and 104 divergent ORFs. 132 divergent ORFs were identified in M. intracellularae. Notably, 104 ORFs were classified as divergent or intermediate in all of the non-paratuberculosis MAC mycobacteria. Many of these ORFs were clustered together on the genome in regions with relatively low average GC content compared to the entire genome. Our results indicate there is a high degree of conservation among bovine M. paratuberculosis isolates that extends to the level of individual genes, while closely related non-paratuberculosis MAC mycobacteria can be distinguished from M. paratuberculosis by multiple clusters of divergent ORFs.